From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Apr 17 2009 - 14:44:11 CDT
You can check that the "NCRTERM" section at the end of the file is
intact. Actually, looking at the source code, it seems that NAMD
ignores the CMAP keyword on the first line anyway, so as log as the
last section is present, cross-terms should be properly included. To
check for this, just look at the "Structure Summary" section of the
NAMD log file.
2009/4/17 Sébastien Légaré <Sebastien.Legare_at_rsvs.ulaval.ca>:
> Hi Jerome
> I completely missed this. Just to be sure, adding the word "CMAP" on the first
> line of the psf generated by Alchemify will get CMAP included right? Would
> something more be missing?
> On April 16, 2009 08:21:51 pm you wrote:
>> Dear Sebastian,
>> You make a very good point. Alchemify was written back in the days
>> when I didn't worry about CMAP that much. It's silly, because the CMAP
>> section should be copied properly - it's just that the word "CMAP"
>> gets deleted from the first line.
>> Now, this should not be a problem from now on, since NAMD 2.7 makes
>> Alchemify obsolete - everything is handled internally. At this point I
>> should just change all the documentation to tell people *not* to use
>> Thanks for raising this issue...
>> On Thu, Apr 16, 2009 at 8:11 PM, Sebastian Stolzenberg
>> <s.stolzenberg_at_gmail.com> wrote:
>> > Dear Jerome,
>> > from a CMAP-equilibrated system, I have prepared a CMAP FEP initial
>> > structure (psf/pdb), using my own CMAP-hybrid-topology definitions (for
>> > GLU2GLUP).
>> > In this regard, can "alchemify" handle CMAP? The reason I wanted to
>> > double-check with you is that in your "alchemify" C code, I found
>> > commands, writing out "PSF" as first line, regardless of whether the
>> > first input psf line was "PSF" or "PSF CMAP".
>> > Thanks for your help,
>> > Sebastian
> Sébastien Légaré
> Ph. D. Student
> Laval University
> Quebec, Canada, G1V 0A6
> 418-656-2131 #11577
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